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package/MDAnalysis/analysis Expand file tree Collapse file tree Original file line number Diff line number Diff line change 7272 :class:`~MDAnalysis.transformations.nojump.NoJump`
7373 transformation to unwrap coordinates on-the-fly.
7474
75- A minimal example:
76-
77- .. code-block:: python
78-
79- import MDAnalysis as mda
80- from MDAnalysis.transformations import NoJump
81-
82- u = mda.Universe(TOP, TRAJ)
83-
84- # Apply NoJump transformation to unwrap coordinates
85- u.trajectory.add_transformations(NoJump(u))
86-
87- # Now the trajectory is unwrapped and MSD can be computed normally:
88- from MDAnalysis.analysis.msd import EinsteinMSD
89- MSD = EinsteinMSD(u, select="all", msd_type="xyz")
90- MSD.run()
91-
75+ A minimal example:
76+
77+ .. code-block:: python
78+
79+ import MDAnalysis as mda
80+ from MDAnalysis.transformations import NoJump
81+
82+ u = mda.Universe(TOP, TRAJ)
83+
84+ # Apply NoJump transformation to unwrap coordinates
85+ u.trajectory.add_transformations(NoJump(u))
86+
87+ # Now the trajectory is unwrapped and MSD can be computed normally:
88+ from MDAnalysis.analysis.msd import EinsteinMSD
89+ MSD = EinsteinMSD(u, select="all", msd_type="xyz")
90+ MSD.run()
91+
9292 This example assumes that the trajectory contains periodic box
9393 dimensions. If no periodic boundary information is present, box
9494 dimensions must be defined before applying ``NoJump``, which can
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